Organism : Clostridium acetobutylicum | Module List:
Module 345 Profile

GeneModule member RegulatorRegulator MotifMotif
Network Help

A network view of the module is created using cytoscapeWeb and enables dynamic, interactive exploration of the module properties. In this view, module member genes, motifs, and regulatory influences are represented as peripheral nodes connected to core module node via edges.

Module members are green circles, regulators are red triangles and motifs are blue diamonds. Selection of a node gives access to detailed information in a pop-up window, which allows dragging and pinning to compare multiple selections. Selecting module members will show information about the selected gene such as name, species and fucntions. Motif selection will show motif logo image and e-values. Bicluster selction will show expression profile and summary statistics for the module.

GeneModule member RegulatorRegulator MotifMotif
Regulators for Module 345

There are 8 regulatory influences for Module 345

Regulator Table (8)
Regulator Name Type
CAC2608 tf
CAC3424 tf
CAC1264 tf
CAC1950 tf
CAC3611 tf
CAC2773 tf
CAC1696 tf
CAC2055 tf

Regulator Help

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type.

tf: Transcription factor

ef: Environmental factor

combiner: Combinatorial influence of a tf or an ef through logic gate. Table is sortable by clicking on the arrows next to column headers.

Motif information (de novo identified motifs for modules)

There are 2 motifs predicted.

Motif Table (2)
Motif Id e-value Consensus Motif Logo
7342 1.60e-09 aAGGgGGA
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7343 7.90e+03 GCTTcGGC
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment

Regulon 345 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Function unknown cog subcategory 1.77e-02 2.94e-02 5/29
Functions Help

Biological networks contain sets of regulatory units called functional modules that together play a role in regulation of specific functional processes. Connections between different modules in the network can help identify regulatory relationships such as hierarchy and epistasis. In addition, associating functions with modules enables putative assignment of functions to hypothetical genes. It is therefore essential to identify functional enrichment of modules within the regulatory network.

Functional annotations from single sources are often either not available or not complete. Therefore, we integrated KEGG pathway, Gene Ontology, TIGRFam and COG information as references for functional enrichment analysis.

We use hypergeometric p-values to identify significant overlaps between co-regulated module members and genes assigned to a particular functional annotation category. P-values are corrected for multiple comparisons by using Benjamini-Hochberg correction and filtered for p-values ≤ 0.05.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Members for Module 345

There are 29 genes in Module 345

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0148 CAC0148 CDS None chromosome 153410 154096 + Predicted enzyme with TIM-barrel fold (NCBI ptt file) False
CAC0160 CAC0160 CDS None chromosome 182984 183433 + Predicted acetyltransferase (NCBI ptt file) False
CAC0177 appB CDS None chromosome 200978 201946 + Oligopeptide transport permease protein (NCBI ptt file) False
CAC0352 CAC0352 CDS None chromosome 406790 407467 - Uncharacterized conserved membrane protein, SANA family (NCBI ptt file) False
CAC0746 CAC0746 CDS None chromosome 866550 868895 - Secreted protease metal-dependent protease (NCBI ptt file) False
CAC0994 CAC0994 CDS None chromosome 1141644 1141991 - Predicted membrane protein (NCBI ptt file) False
CAC0995 CAC0995 CDS None chromosome 1142139 1142636 - Predicted membrane protein (NCBI ptt file) False
CAC1160 CAC1160 CDS None chromosome 1322089 1322412 + Hypothetical protein (NCBI ptt file) False
CAC1266 CAC1266 CDS None chromosome 1408461 1409360 + Pseudouridylate synthase family protein, yabo B.subtilis ortholog (NCBI ptt file) False
CAC1450 CAC1450 CDS None chromosome 1598349 1599083 + Predicted alpha/beta superfamily hydrolase (NCBI ptt file) False
CAC1592 CAC1592 CDS None chromosome 1736263 1737366 - Predicted permease, YCGR B.subtilis ortholog (NCBI ptt file) False
CAC1791 CAC1791 CDS None chromosome 1940512 1941285 + Undecaprenyl pyrophosphate synthase (NCBI ptt file) False
CAC1911 CAC1911 CDS None chromosome 2050591 2050812 + Hypothetical protein (NCBI ptt file) False
CAC1950 CAC1950 CDS None chromosome 2067822 2068034 + Hypothetical protein (NCBI ptt file) True
CAC2055 CAC2055 CDS None chromosome 2160782 2161192 + Predicted transcriptional regulator (NCBI ptt file) True
CAC2168 CAC2168 CDS None chromosome 2257365 2259101 - Uncharacterized conserved protein (NCBI ptt file) False
CAC2287 CAC2287 CDS None chromosome 2389911 2391266 - Acyl-CoA reductase LuxC (NCBI ptt file) False
CAC2298 CAC2298 CDS None chromosome 2401052 2401948 - Predicted nucleotidyltransferase (NCBI ptt file) False
CAC2301 mrcB CDS None chromosome 2404758 2407187 + Membrane carboxypeptidase mrcB (NCBI ptt file) False
CAC2343 CAC2343 CDS None chromosome 2454438 2454986 - LPS biosynthesis O-acetyl transferase (NCBI ptt file) False
CAC2414 CAC2414 CDS None chromosome 2531318 2532901 - Uncharacterized conserved protein, related to alpha-amylase/alpha-mannosidase (NCBI ptt file) False
CAC2660 pykA CDS None chromosome 2773031 2776465 - Pyruvate carboxylase, PYKA (NCBI ptt file) False
CAC2687 recQ CDS None chromosome 2808658 2810802 + RecQ protein, superfamily II DNA helicase (NCBI ptt file) False
CAC2694 CAC2694 CDS None chromosome 2816779 2816940 - Hypothetical protein (NCBI ptt file) False
CAC2781 CAC2781 CDS None chromosome 2911603 2912145 + Hypothetical protein (NCBI ptt file) False
CAC2946 CAC2946 CDS None chromosome 3078767 3079159 - Hypothetical protein (NCBI ptt file) False
CAC2961 galT CDS None chromosome 3094510 3096003 + Galactose-1-phosphate uridyltransferase (NCBI ptt file) False
CAC2988 CAC2988 CDS None chromosome 3124747 3125880 - Uncharacterized conserved protein, YABE B.subtilis ortholog (NCBI ptt file) False
CAC3424 CAC3424 CDS None chromosome 3610162 3610869 + Transcriptional regulator, RpiR family (NCBI ptt file) True

Genes Help

Gene member table shows all the genes included in the module. Listed attributes are;

  1. Name: Gene name or Locus tag
  2. Common Name: Gene short name
  3. Type: Type of the feature, usually CDS.
  4. Gene ID: Link to NCBI Gene ID
  5. Chromosome: Chromosome name from annotation file
  6. Start/End:Feature start and end coordinates
  7. Strand: strand of the gene
  8. Description: Description of the gene from annotation file
  9. TF: If the gene is a Transcription Factor or not.

If you are browsing the Network Portal by using Gaggle/Firegoose, firegoose plugin will capture the NameList of the gene members. Captured names can be saved into your Workspace by clicking on "Capture" in the firegoose toolbar or can be directly sent other desktop and web resources by using "Broadcast" option.

Help

What is a module?

Regulatory units (modules) in the Network Portal are based on the network inference algorithm used. For the current version, modules are based on cMonkey modules and Inferelator regulatory influences on these modules. More specifically, module refers to set of genes that are conditionally co-regulated under subset of the conditions. Identification of modules integrates co-expression, de-novo motif identification, and other functional associations such as operon information and protein-protein interactions.

Module Overview

The landing module page shows quick summary info including co-expression profiles, de-novo identified motifs, and transcription factors and/or environmental factors as regulatory influences. It also includes module residual, motif e-values, conditions and links to other resources such as NCBI and Microbesonline. . If a transcription factor is included in the manually curated RegPrecise database, further information from RegPrecise is shown, allowing users to perform comparative analysis.

Expression Profiles

Expression profiles is a plot of the expression ratios (log10) of the module's genes, over all subset of the conditions included in the module. The X-axis represent conditions and the Y-axis represents log10 expression ratios. Each gene is plotted as line plot with different colors. Colored legend for the lines are presented under the plot. This plot is dynamic. Clicking on the gene names in the legend will show/hide the plot for that particular gene. A tooltip will show expression ratio information if you mouseover the lines in the plot.

Motif Locations

Location of the Identified motifs for the module in the upstream regions of the member genes are shown under the expression profiles plot. This plot shows the diagram of the upstream positions of the motifs, colored red and green for motifs #1, and 2, respectively. Intensity of the color is proportional to the significance of the occurence of that motif at a given location. Motifs on the forward and reverse strand are represented over and under the line respectively.

Network

A network view of the module is created using cytoscapeWeb and enables dynamic, interactive exploration of the module properties. In this view, module member genes, motifs, and regulatory influences are represented as peripheral nodes connected to core module node via edges. Module members are green circles, regulators are red triangles and motifs are blue diamonds. Selection of a node gives access to detailed information in a pop-up window, which allows dragging and pinning to compare multiple selections. Selecting module members will show information about the selected gene such as name, species and fucntions. Motif selection will show motif logo image and e-values. Bicluster selction will show expression profile and summary statistics for the module.

GeneModule member RegulatorRegulator MotifMotif

Regulators

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type. tf: Transcription factor, ef: Environmental factor and combiner:Combinatorial influence of a tf or an ef through logic gate. Tabel is sortable by clicking on the arrows next to column headers.

Motifs

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Functions

Biological networks contain sets of regulatory units called functional modules that together play a role in regulation of specific functional processes. Connections between different modules in the network can help identify regulatory relationships such as hierarchy and epistasis. In addition, associating functions with modules enables putative assignment of functions to hypothetical genes. It is therefore essential to identify functional enrichment of modules within the regulatory network.

Functional annotations from single sources are often either not available or not complete. Therefore, we integrated KEGG pathway, Gene Ontology, TIGRFam and COG information as references for functional enrichment analysis.

We use hypergeometric p-values to identify significant overlaps between co-regulated module members and genes assigned to a particular functional annotation category. P-values are corrected for multiple comparisons by using Benjamini-Hochberg correction and filtered for p-values ≤ 0.05.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Genes

Gene member table shows all the genes included in the module. Listed attributes are;

  1. Name: Gene name or Locus tag
  2. Common Name: Gene short name
  3. Type: Type of the feature, usually CDS.
  4. Gene ID: Link to NCBI Gene ID
  5. Chromosome: Chromosome name from annotation file
  6. Start/End:Feature start and end coordinates
  7. Strand: strand of the gene
  8. Description: Description of the gene from annotation file
  9. TF: If the gene is a Transcription Factor or not.

If you are browsing the Network Portal by using Gaggle/Firegoose, firegoose plugin will capture the NameList of the gene members. Captured names can be saved into your Workspace by clicking on "Capture" in the firegoose toolbar or can be directly sent other desktop and web resources by using "Broadcast" option.

Social

You can start a conversation about this module or join the existing discussion by adding your comments. In order to be able to add your comments you need to sign in by using any of the following services;Disqus, Google, Facebook or Twitter. For full compatibility with other network portal features, we recommend using your Google ID.

Definitions

Residual: is a measure of bicluster quality. Mean bicluster residual is smaller when the expression profile of the genes in the module is "tighter". So smaller residuals are usually indicative of better bicluster quality.

Expression Profile: is a preview of the expression profiles of all the genes under subset of conditions included in the module. Tighter expression profiles are usually indicative of better bicluster quality.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Genes: Number of genes included in the module.

Functions: We identify functional enrichment of each module by camparing to different functional categories such as KEGG, COG, GO etc. by using hypergeometric function. If the module is significantly enriched for any of the functions, this column will list few of the these functions as an overview. Full list of functions is available upon visiting the module page under the Functions tab.